`prune_vertices`

removes vertices from a neuron

`prune_edges`

removes edges (and any unreferenced vertices)

prune_vertices(x, verticestoprune, invert = FALSE, ...) prune_edges(x, edges, invert = FALSE, ...)

x | A |
---|---|

verticestoprune | An integer vector describing which vertices to remove. |

invert | Whether to keep vertices rather than dropping them (default FALSE). |

... | Additional arguments passed to |

edges | The edges to remove. One of i) an Nx2 matrix, each row
specifying a single edge defined by its |

A pruned `neuron`

These are relatively low-level functions and you will probably want
to use `subset.neuron`

or `prune.neuron`

and
friends in many cases.

Note that `prune_vertices`

and `prune_edges`

both use **raw**
vertex ids to specify the vertices/edges to be removed. If you want to use
the id in the PointNo field, then you must translate yourself (see
examples).

Both `prune_vertices`

and `prune_edges`

first convert their input
`x`

to the `ngraph`

representation of the neuron before
removing points. The input `x`

can therefore be in any form compatible
with `as.ngraph`

including an existing `ngraph`

. There is
an additional requirement that the input must be compatible with
`xyzmatrix`

if `invert=TRUE`

.

Note that the `edges`

argument of `prune_edges`

must specify a
path traversing a set of vertices in a valid order. However if the input is
a matrix or vector the direction of each individual edge in this path is
ignored. So if your neuron has edges 2->1 2->3 3->4 then an edge sequence
1:3 would successfully delete 2 edges.

# use the PointNo field (= the original id from an SWC file) n2=prune_vertices(n, match(26:30, n$d$PointNo)) y=prune_edges(Cell07PNs[[1]], edges=1:25) # remove the spine of a neuron spine_ids=spine(Cell07PNs[[1]], rval='ids') pruned=prune_edges(Cell07PNs[[1]], spine_ids) # NB this is subtly different from this, which removes vertices along the # spine *even* if they are part of an edge that is outside the spine. pruned2=prune_vertices(Cell07PNs[[1]], spine_ids)